title: Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop.
abstract: Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexibility of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free-energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially "locks" the kinase into its catalytically competent conformation.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Yilin
authors.initials: Y
authors.lastname: Meng
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA. Electronic address: roux@uchicago.edu.
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
mesh_terms: D000595:Amino Acid Sequence; D000081247:CSK Tyrosine-Protein Kinase; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D014443:Tyrosine / Q000378:metabolism; D019061:src-Family Kinases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D014443:Tyrosine; D000081247:CSK Tyrosine-Protein Kinase; D019061:src-Family Kinases
keywords: MD; MFEP; PMF; SFK; SH2; SH3; Src family kinase; Src-homology 2; Src-homology 3; US; activation loop; c-Src kinase; free-energy landscapes; minimum free-energy pathway; molecular dynamics; phosphorylation; potential of mean force; umbrella sampling; wild type; wt